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revision 1.1222 by jmc, Wed Jan 20 04:11:33 2010 UTC revision 1.1304 by mlosch, Sat Sep 25 23:10:51 2010 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o momentum:  o add hooks for new packages OASIS, the package will follow
8      (hooks exclude the seaice pkg for now)
9    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
10      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
11      rather than mdsio_readvector.F/mdsio_writevector.F, within
12      adread_adwrite.F to read/write adjoint-related tapes to disk.
13    o eesup and pkg/mdsio: ALLOW_WHIO
14    
15      Option to write/read 2D fields to files including tiles halos.
16      The main purpose is for adjoint related "tape I/O".
17      The secondary purpose is for debugging phases.
18    
19      A word on those rather specifically intended purposes.
20      The code was meant to be stripped down to the bare minimum.
21      Typically, there is a unique and basic mapping to the global
22      buffer (tile by tile, then proc by proc, then level by level), and
23      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
24      meant to generate user friendly outputs of various shapes and forms.
25      Rather it is intended, for the knowledgeabale developers,
26      to be largely independent of the many mdsio options, to allow
27      outputs of tiles+halos in debugging phases and in adjoint runs,
28      and to allow some flexibility in tuning (adoint) I/O depending on each
29      file system behavior. With regard to tuning, most of the potential knobs
30      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
31      to specify directories, to specify the typical size of I/O calls, etc.)
32      are not yet included, and will be added if they prove useful.
33    o pkg/seaice:
34       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
35    o pkg/seaice:
36       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
37       code (seaice_budget_ice_if.F) which enable to recover old standard
38       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
39       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
40    o model/src (rStar):
41       use simple average (not area weighted) of rStarFac at U,V point when using
42       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
43       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
44    
45    checkpoint62k (2010/09/17)
46    o adjoint
47       * changed verification/global_ocean.cs32x15 ; adjoint now tests
48         Adams-Bashforth 3 + NLFS + RSTAR
49       * some more modifs required for ECCO-GODAE v4
50    o pkg/seaice
51       add SEAICE_AGE_VOL option to use volume instead of area for
52       integrating SEAICE_AGE
53    o model/src:
54       first check-in of sigma & hybrid-sigma coordinate code ; also includes
55       non-linear free-surface parts ; but pressure-gradient not yet coded.
56    o pkg/ptracers:
57       option for ptracer to convert Salt Relax into additional EmP.
58        tested in exp. global_ocean.90x40x15.dwnslp (update output)
59    
60    checkpoint62j (2010/08/25)
61    o pkg/ggl90:
62       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
63    o pkg/dic: car_flux.F, phos_flux.F
64      - reduce number of exp-calls in order to improve performance
65      - clean up a little (replace fields by their macros, etc., fix
66        typo in CPP-flag)
67    o pkg/ggl90: minor changes
68      - GGL90diffKrS was removed --> always use GGL90diffKr
69      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
70      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
71        (commented out for now)
72      - change in max/min operations to ensure that smoothing is ok
73      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
74      - always use diffKrNrT as background profile (i.e. never use diffKr field)
75    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
76    o pkg/dic:
77      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
78        vectorization
79      - small bug fix in insol for the unlikely case of a cartesian grid
80      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
81        + now vectorize, which also removes adjoint recomputations;
82        + replace integer maksp1 by _RL maskp1
83        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
84    
85    checkpoint62i (2010/07/21)
86    o pkg/flt:
87      - with OBCS: stop floats which enter the OB region
88    o model/src:
89      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
90        for implicit vertical advection.
91    o pkg/seaice:
92     - account for melting in seaice age evolution.
93     - remove double counting of seaice ridging effect on seaice age.
94    
95    checkpoint62h (2010/06/18)
96    o pkg/exch2:
97     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
98    o tools/genmake2
99      - remove "-pdefault" option: redundant with the use of "packages.conf";
100      - remove file pkg/pkg_default : set the default as a pkg group
101        ("default_pkg_list") defined in pkg/pkg_groups;
102      - fix for case pkg/pkg_depend is missing (was hanging before);
103      - add option "-pgroups" to specify a different pkg_groups than the default.
104    o verification/adjustment.cs-32x32x1:
105       add a "minimal" set-up test (code_min & input_min) which only compiles
106       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
107    o tools/genmake2
108      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
109      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
110    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
111      files are nearly the same anyway.
112      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
113       - redefinition of tau(i,i) (by a factor of ustar)
114       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
115       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
116       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
117       - replace
118         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
119         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
120         by
121         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
122         (changes results)
123       -> exf_bulkformulae v1.22,
124          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
125          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
126                    output.txt 1.63
127           offline_exf_seaice: output.seaicetd.txt 1.7
128           seaice_obcs: output.txt 1.10)
129      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
130       -> exf_bulkformulae v1.23,
131          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
132          and global_ocean.cs32x15.icedyn (only 11 matching digits)
133      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
134    o adjoint of exch-1:
135     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
136       (note: was already like this when using EXCH-2) and remove flow dir
137       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
138     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
139     - update pkg/exch2 diff list.
140    
141    checkpoint62g (2010/05/19)
142    o eesupp/src (exch-1):
143     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
144       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
145       (renamed to exch1_*rx_cube.F).
146     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
147       to call new exch1 S/R ; update Makefile and .cvsignore.
148     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
149       exch2_xy_rx later)
150      Note: after updating your code, need to run "make clean" in eesupp/src
151    o test experiment bottom_ctrl_5x5:
152       new output_adm.txt with fewer grdchk & less monitor output.
153    o model/src:
154      remove the call to ini_cori in initialise_varia.F (just keep the usual one
155       in initialise_fixed.F). More consistent with coriolis & horizontal grid
156       beeing treated in the same way (ini_grid is not called a 2nd time).
157    o pkg/exf:
158      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
159      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
160      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
161      - cosmetic changes to exf_bulkformulae.F to make it look more like
162        exf_bulk_largeyeager04.F
163    o eesupp/src (exch-1):
164      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
165      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
166        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
167        (even without using MPI).
168      - Message mode: move RecvAck setting (indicator of buffer being ready)
169        from send_put to recv_get S/R (was useless before, but not sure if
170        it's much more useful now);
171      - Switch the order of sync: MPI-proc 1rst and then threads;
172      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
173      - fix AD code for communication mode ='get' (but not used).
174    o model/src:
175      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
176      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
177    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
178    o pkg/ctrl: require a specific set of control variables and exf-flags for
179      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
180    o model/src:
181     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
182       1rst forward sweep, to avoid over-writing output files during recomputations
183       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
184     b) 2nd version:
185      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
186      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
187         writePickupAtEnd) + seaice & ptracers output;
188      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
189    o model/src:
190      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
191    o pkg/exch2:
192      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
193      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
194    o pkg/autodiff & exch2:
195      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
196      (for now, only if ALLOW_EXCH2 is defined).
197    o pkg/autodiff:
198      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
199        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
200       + clean-up comments (_RS is not always real*4)
201      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
202      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
203        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
204    o testreport (AD-tests):
205      no longer link files from dir "../input" (1rst link files from
206      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
207    
208    checkpoint62f (2010/04/29)
209    o model/src/the_main_loop.F:
210      adjust store directives for seaice evp and multicategory according to
211      pkg/ecco/the_main_loop.F
212    o adjoint:
213      global_sum_ad was incomplete (noted many times by many people ;)
214      nice description by Jean U. as follows:
215      * allreduce(var) in global_sum.F can be interpreted as
216        reduce(sum) followed by broadcast of sum.
217      * The adjoint of that is
218        sum(adjoint) followed by broadcast(summed adjoint value)
219        or in other words, allreduce(sum, adjoint vars)
220      We were missing the sum(adjoint)!
221      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
222      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
223      The fix should produce 16-digit accuracy between
224      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
225      multi-CPU single-tile (e.g. nSx=1, nPx-2)
226      We'll probably change this yet again shortly
227    o eesupp/src:
228      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
229    o pkg/icefront
230      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
231        specification of addmass array based on a 2D field, which is added
232        at bottommost wet level at each horizontal location.
233    o model/src:
234     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
235     layout; (not always compatible with delX,delY setting; commented out for now).
236    o pkg/exch2:
237     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
238     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
239    
240    checkpoint62e (2010/04/15)
241    o pkg/obcs:
242      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
243    o pkg/dic:
244      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
245        (note: not presently tested in any forward verification exp.)
246       update tutorial_global_oce_biogeo AD output file.
247    o pkg/exf:
248      - account for the variation of albedo as a function of zenith angle
249        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
250    o build_options:
251     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
252    o pkg/dic:
253      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
254      - use binary pickup file for restart;
255      - initialise atmos-CO2 box from dic_pCO2 parameter;
256      - fix multi-threaded.
257    o pkg/rbcs:
258     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
259       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
260     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
261       and update output.txt
262    o pkg/kpp:
263     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
264     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
265       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
266       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
267     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
268       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
269    o pkg/offline:
270      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
271      (bug was added in version 1.10 on 2007-08-23).
272    o pkg/offline:
273      - no need to specify periodicExternalForcing, etc ... to use offline pack
274      - offline input files no longer just single prec --> parameter offlineLoadPrec
275    o verification/lab_sea:
276      change AD test to multi-tile setup and update all 4 AD output.
277      NOTE: while cost function values remain very similar,
278      gradients are very different, although gradient checks are self-consistent
279      Should try to get to the bottom of this (cost function summation order?)
280    o pkg/dic:
281      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
282      a weakness of TAF that drops part of double precision in log10 derivative.
283      <= changes removed since problem has been fixed in current TAF version 1.9.71
284      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
285    o pkg/ecco:
286      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
287      update all 4 lab_sea AD output.
288    
289    checkpoint62d (2010/03/22)
290    o build_options:
291      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
292    o remove unbalanced quote (single or double) in commented line of source code
293      (may cause some warning with some preprocessor/makedepend versions).
294    o pkg/seaice:
295      fix seaice_model.F for adjoint (gael) and update AD results of experiments
296       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
297    o testreport:
298      add option '-runonly' (short: '-ro') to just do the run part (without make).
299    o eesupp: remove JAM communication code (obsolete).
300    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
301      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
302      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
303      (update also the output).
304    
305    checkpoint62c (2010/03/02)
306    o tools/build_options :
307       move (some) old optfiles from build_options/ to build_options/unsupported/
308    o model/src and pkg/exf
309       surface relaxation -- separating data and data.exf options
310       The point is to ensure that we specify the surface relaxation
311       either in data or in data.exf (but not half and half) and to
312       avoid an accidental relaxation to 0 (which happened if a time
313       scale was specified but the file name was left empty)
314    o model/src model/inc and pkg/mom_common
315       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
316       => addition to the viscosity field as computed by others schemes
317    o tools/build_options:
318      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
319        but keep the former optfile for few weeks for smooth transition
320    o pkg/ecco
321      - allow user defined cost function contributions
322            CPP: ALLOW_USERCOST_CONTRIBUTION
323            USAGE: compute contributions in cost_usercost_all.F
324      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
325          the two options are complementary.
326    o pkg/smooth
327      - migration from contrib to the main repository
328    
329    checkpoint62b (2010/01/26)
330    o pkg/monitor:
331      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
332        (in case someone forgot to update customized pieces of code)
333    o nonHydrostatic:
334      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
335      - add a simple 2-D experiment (short_surf_wave) to test it.
336    o pkg/icefront:
337       adding the shell of, and the hooks to, a new package that
338       will model melting and freezing of vertical glacier ice fronts
339    o momentum:
340    add diagnostics of momentum tendency from Hydrostatic pressure gradient    add diagnostics of momentum tendency from Hydrostatic pressure gradient
341     (without surf.pressure term: would need a 2nd filling since implicit term).     (without surf.pressure term: would need a 2nd filling since implicit term).
342  o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace  o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
343    two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR    two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
344    cannot deal with the former    cannot deal with the former
345  o cleaning:  o cleaning:
346    - remove all (except OpenAD) old TLM output from results_ad dirs.    - remove all (except OpenAD) old TLM output from results_ad dirs.
347    - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)    - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
348    - comment out maskH definition (replaced by maskInC)    - comment out maskH definition (replaced by maskInC)
349  o pkg/monitor:  o pkg/monitor:
350    - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl    - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
351      & mon_calc_stats_rl) to be the RL pendant to mon_printstats_rs & mon_stats_rs.      & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
352    
353  checkpoint62a (2010/01/15)  checkpoint62a (2010/01/15)
354  o model/src:  o model/src:

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